OTTAWA — Civil servants who transfer between federal departments or receive promotions can expect to wait more than six months for their paycheques to follow them through the Phoenix pay system, federal officials say, costing some employees tens of thousands of dollars as they wait — and causing confusion across government.

But the problem is far worse than the Liberals are letting on, with many people now refusing to take promotions and parental leave over fears that they'll lose their paycheques entirely, says the union representing a majority of government workers.

The average wait time to process an employee transfer from one department to another was about 136 working days as of mid-January, said Public Services and Procurement Canada, which is responsible for the pay system.

But some government employees have been told it could take up to a year or longer to have their transfers completed.

"We've certainly heard much worse," said Chris Aylward, national executive vice-president of the Public Service Alliance of Canada.

"We've heard of up to a year, especially when people transfer from one department to another."

It is especially frustrating for those who are promoted into higher-paid positions, only to be told they'll have to wait months for pay increases while performing in jobs that are often more stressful.

"We acknowledge that this situation is frustrating and poses challenges, Public Services said in an email.

"However, employees continue to receive their pay from their former department until the transfer of their pay to their new department is complete," the department said.

Transfer wait times ballooned over the last year as the government placed a greater priority on ensuring that civil servants who were underpaid — or not paid at all — were receiving the remuneration they were owed.

Between Jan. 1, 2015 and Dec. 31, 2015 — prior to the launch of the Phoenix pay system — the average wait time to process an employee transfer from one department to another was just 17 working days, or less than a month, Public Services and Procurement Canada said in an email.

The following year, while the Phoenix system was being brought online, the average wait time to complete pay transfers nearly tripled, to 45 working days.

Phoenix was launched in two phases in 2016, first across fewer than three dozen departments in late February of that year.

The second phase was unleashed across another 67 departments in April, 2016, even as civil service unions and the government were being flooded with stories of employees with difficulties being paid. By summer of that year, the government acknowledged some 80,000 civil servants were experiencing significant pay issues.

Despite early predictions that the system would be fixed within months, the problems have not only persisted, they have grown substantially with the overall number of civil servants impacted with pay issues approaching 200,000 by the end of 2017, according to the department.

Public Services said it is now treating employee transfer backlog as a priority and hopes to develop a new regime in place this year to address it.

"Re-designing the employee transfer process is recognized as a priority and is being addressed through the HR-to-Pay initiative in early 2018," the department said in an email.

Aylward scoffed at the notion.

"They say the overpayments are a priority, doing the T4s are a priority, implementing the collective agreements are priorities and now they're saying transfers from one department to another is a priority," he said.

"Everything is a priority, and therefore nothing is a priority. That's our concern."

The pay transfer delays have also muddied the books in federal departments that are continuing to count the salaries for employees who have moved on to other jobs.

Department managers are left paying the salaries of employees who no longer work for them and in some instances they are paying two salaries for one position when they hire to replace people who have left. Or, they simply don't hire someone to replace a departed employee until their pay file is finally transferred, said Aylward.

"Their salary budgets are completely out of whack. I don't know how departments are managing."

Union and government officials met the federal Public Service Labour Relations Board Jan. 31, where the Treasury Board Secretariat acknowledged the government failed to meet deadlines for implementing four collective agreements. PSAC has asked the board to award public servants damages for breaching the deadlines spelled out in those agreements, which were signed by the government in June.

The board is now expected to issue a directive forcing Ottawa to fully implement the agreements, although it's unclear what impact, if any, such an order will have on employees.